[gmx-users] Gromacs Group Project Force-Field Query

[Justin Lemkul]

On 2/15/19 8:39 AM, Matthew Atkinson wrote:
> Dear all,
>
> We are currently working on a project at the University of Manchester, which involves using GROMACS to understand the molecular dynamics of the biological machines for the walkers dynein and kinesin. However, when using the command gmx_d pdb2gmx -f 5nvu_clean.pdb -o 5nvu_processed.gro -water spce and selecting force field any force field 1-15, a resulting error “residue ‘UNK’ not found in residue topology” occurs. After searching and applying many solutions, a fatal error still occurs, what would you suggest we do? Would there be a force field not listed that we could use? The protein ID’s used are 5NVU and 3U06.

You have a nonstandard residue that the force field doesn't recognize. 
You should check the PDB file for comments about what it is and if it is 
actually biologically relevant. If it's not, delete it (these are often 
crystallization cosolvents, crosslinkers, etc. that are not actually 
real) but if it is, you have to parametrize it using some external tools 
in a manner consistent with the parent force field you're trying to use.

-Justin

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Justin A. Lemkul, Ph.D.
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